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NCBI C++ ToolKit: src/algo/ms/omssa/msladder.cpp Source File

Ladder(new

[SizeIn]),

Hit(new

[SizeIn]),

Intensity(new unsigned[SizeIn]),

Delta(new

[SizeIn]),

Ladder(new

[Old.LadderSize]),

Hit(new

[Old.LadderSize]),

LadderSize(Old.LadderSize)

(

= 0;

<

();

++) {

ModMask,

ModList[],

*IntMassArray = MassArray.

();

*

AAMap(AA.

());

ProlineOffset(0);

, Direction, NumMod, ModIndex,

ModList, ModMask, 0, ion,

, SearchType,

ExactMass))

;

ModIndex = NumMod - 1;

, Direction, NumMod, ModIndex,

ModList, ModMask, 0, ion,

, SearchType,

ExactMass))

;

, Direction, NumMod, ModIndex,

ModList, ModMask,

+iSkip, ion,

, SearchType,

ExactMass))

;

(

+ iSkip + ProlineOffset <= stop - start &&

[

+ Direction * (

+ iSkip + ProlineOffset)] !=

)) {

(

() !=

(

-

))

;

((*

)[

] <= MassIndex + Tolerance &&

(*

)[

] > MassIndex - Tolerance )

;

((*

)[x] < MassIndex - Tolerance)

((*

)[x] > MassIndex + Tolerance)

(x < LadderIndex - 1 && x >= 0 &&

(*

)[x+1] < MassIndex + Tolerance && (*this)[x+1] >

MassIndex - Tolerance)

TSeriesChargePairList::iterator Iter;

(

= 0;

< MaxModPerPep;

++) {

newLadderListPtr->push_back(newLadder);

(BeginCharge != 0 && EndCharge != 0) {

!

(Iter, BeginCharge, EndCharge, SeriesType))

(

(Iter, BeginCharge, EndCharge, SeriesType))

;

(Iter, BeginCharge ,EndCharge, SeriesType);

const char *const GetMap(void) const

return the map for translating AA char to AA number

void Next(TLadderMap::iterator &Iter, TMSCharge BeginCharge=0, TMSCharge EndCharge=0, TMSIonSeries SeriesType=eMSIonTypeUnknown)

iterate over the ladder map over the charge range and series type indicated

TSeriesChargePairList & SetSeriesChargePairList(void)

return the list of charge, series type pairs that are used to initialize the maps

void Begin(TLadderMap::iterator &Iter, TMSCharge BeginCharge=0, TMSCharge EndCharge=0, TMSIonSeries SeriesType=eMSIonTypeUnknown)

bool MatchIter(TLadderMap::iterator &Iter, TMSCharge BeginCharge=0, TMSCharge EndCharge=0, TMSIonSeries SeriesType=eMSIonTypeUnknown)

see if key of the map element pointed to by Iter matches the conditions

void CreateLadderArrays(int MaxModPerPep, int MaxLadderSize)

populate the Ladder Map with arrays based on the ladder

TLadderMap & SetLadderMap(void)

returns the laddermap (maps key based on charge and series type to a vector of CLadder)

bool Contains(int MassIndex, int Tolerance)

TIntensity & SetIntensity(void)

Set the intensity array.

const TDelta & GetDelta(void) const

Get the mass delta array.

bool CalcDelta(const int *IntMassArray, const char *const AAMap, const char *Sequence, int Offset, int Direction, int NumMod, int &ModIndex, const CMod ModList[], unsigned ModMask, int i, int &ion, const int ChargeIn, EMSSearchType SearchType, double ExactMass)

calculate the mass difference

const bool CreateLadder(const int IonType, const int Charge, const char *const Sequence, const int SeqIndex, const int start, const int stop, const int mass, const CMassArray &MassArray, const CAA &AA, const unsigned ModMask, const CMod ModList[], const int NumMod, const CMSSearchSettings &Settings, const bool NoProline)

make a ladder

const TIntensity & GetIntensity(void) const

Get the intensity array.

AutoPtr< int, ArrayDeleter< int > > Ladder

mass ladder

AutoPtr< THit, ArrayDeleter< THit > > Hit

hit count for a given m/z value

bool ContainsFast(int MassIndex, int Tolerance)

void Or(CLadder &LadderIn)

TLadderNumber & SetLadderNumber(void)

Return the array containing the number of the ions.

TDelta & SetDelta(void)

Set the mass delta array.

int Sum

sum of ranks of matched peaks

const TLadderNumber & GetLadderNumber(void) const

Return the array containing the number of the ions.

int M

number of matched peaks

static const int ChargeSeries2Key(TMSCharge Charge, TMSIonSeries Series)

convert a charge and series to a map key

static const TMSIonSeries Key2Series(int Key)

convert a key into a series type

static const TMSCharge Key2Charge(int Key)

convert a key into a charge

@MSSearchSettings.hpp User-defined methods of the data storage class.

const int *const GetIntMass(void) const

contains information for a post translational modification at a particular sequence site

container_type::iterator iterator

const_iterator begin() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

Include a standard set of the NCBI C++ Toolkit most basic headers.

element_type * get(void) const

Get pointer.

void Reset(void)

Reset reference object.

TNegative GetNegative(void) const

Get the Negative member data.

TSearchb1 GetSearchb1(void) const

Get the Searchb1 member data.

EMSSearchType

what type of atomic mass to use

TProductsearchtype GetProductsearchtype(void) const

Get the Productsearchtype member data.

const TChargehandling & GetChargehandling(void) const

Get the Chargehandling member data.

TExactmass GetExactmass(void) const

Get the Exactmass member data.

TSearchctermproduct GetSearchctermproduct(void) const

Get the Searchctermproduct member data.

unsigned int

A callback function used to compare two keys in a database.

vector< CRef< CLadder > > TLadderList

const double kIonTypeMass[]

const int kIonDirection[]

ion direction.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

signed char TMSCharge

charge type

short TMSNumber

ion sequence number, starting from 0.

signed char TMSIonSeries

ion type, e.g.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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